Open rafwiewiora opened 8 years ago
Can you post the PDB file where it doesn't recognize the residue as nonstandard?
Here! https://gist.github.com/rafwiewiora/41ebf2022e14836063dda156891c3c68 (the test case above - test.pdb)
And here the pdb which was of interest to me (described in the first paragraph above): https://gist.github.com/rafwiewiora/f73f22eca5708408652f0bd4972d579e
This is my work sequence: take 2BQZ, delete half of chains with pdbfixer, save, add H's with REDUCE (http://kinemage.biochem.duke.edu/software/reduce.php - but not important here), then I wanted to re-use pdbfixer and mutate a non-standard methyl-lysine to lysine. At this point, however,
findMissingResidues()
no longer identifies the methyl-lysine (MLZ) as a non-standard residue.This does not appear to have anything to do with my adding H's in a different software. A test case:
simple pass through the pdbfixer makes
findNonstandardResidues()
not work on the second go.